Figure 2.

Longer doubling times of simulated cells with operons suggested an alternative transcription unit structure for the rplKAJL-rpoBC operon. See also Figure S1. (A) An example of how gene-level RNA-Seq read counts were translated into transcript-level RNA-Seq read counts using transcription unit (TU) structures and nonnegative least squares (NNLS). (B) Comparison of simulated doubling times in rich media conditions between simulations with and without operons after the initial integration of transcription unit structures from RegulonDB/EcoCyc. Simulations with operons had longer doubling times on average (38.3 ± 4.9 mins, n=964, where n is the number of simulated cells with fully completed cell cycles) compared to simulations without operons (27.2 ± 11.1 mins, n=999). (C) Comparison of mean mRNA copy numbers for genes encoding for subunits of RNAPs and ribosomes in rich media conditions between the two simulations. Copy numbers were calculated by averaging the copy numbers from the first timesteps of simulated cells with fully completed cell cycles, excluding cells from the first two generations (n=743 for simulations without operons, n=715 for simulations with operons). (D) The transcription unit structure for the rplKAJL-rpoBC operon suggested by RegulonDB/EcoCyc. This transcription unit structure was not cross-consistent with the RNA-Seq read counts of the genes in the operon. (E) Rend-seq data for the rplKAJL-rpoBC operon³². A 3’-end peak is clearly visible downstream of gene rplL (arrow), suggesting the existence of a transcriptional terminator that is missing from RegulonDB/EcoCyc. Other 5’-end and 3’-end peaks in the Rend-seq data align well with existing promoters/terminators in RegulonDB/EcoCyc. (F) Additional transcription units (red) proposed for the rplKAJL-rpoBC operon based on Rend-seq data. The addition of these transcription units allows the NNLS algorithm to find a solution that aligns better with the gene-level RNA-Seq read counts. (G) Comparison of mean mRNA copy numbers for genes encoding for subunits of RNAPs and ribosomes in rich media conditions after adding the two transcription units suggested by Rend-seq data. Copy numbers were calculated by averaging the copy numbers from the first timesteps of simulated cells with fully completed cell cycles, excluding cells from the first two generations (n=743 for simulations without operons, n=731 for simulations with operons). (H) Comparison of simulated doubling times in rich media conditions after adding the two transcription units. Simulations with operons had doubling times (28.2 ± 8.1 mins, n=981, where n is the number of simulated cells with fully completed cell cycles) that are similar to simulations without operons (27.2 ± 11.1 mins, n=999).